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2001 Fiscal Year Final Research Report Summary

Mechanism of Triplex DNA Formation ; And Its Application to Antisense

Research Project

Project/Area Number 09558090
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section展開研究
Research Field Functional biochemistry
Research InstitutionRIKEN Insutitute

Principal Investigator

SARAI Akinori  RIKEN, Insutitute, Senior Scientist, 分子遺伝学研究室, 副主任研究員 (20221286)

Co-Investigator(Kenkyū-buntansha) PICHIERRI Fabio  RIKEN, Insutitute, Scientist, 情報伝達モデル化研究チーム, 研究員
TORIGOE Hidetaka  RIKEN, Insutitute, Senior Scientist, 細胞生理学研究室, 先任研究員 (80227678)
YOKOYAMA Kazunari  RIKEN, Insutitute, Senior Scientist, 遺伝子材料開発室, 副主任研究員 (80182707)
SINDO Heisaburo  TOKYO UNIVERSITY OF PHARMACY, PROFESSOR, 薬学部, 教授 (80138966)
Project Period (FY) 1997 – 2000
KeywordsTriplex DNA / Thermodynamics / Computer simulation / Antisense
Research Abstract

In order to understand the mechanism of stability and specificity in triplex DNA formation, we performed experimental and computational analyses. We synthesized DNA with chemical modifications at different locations, and measured thermodynamic quantities such as dissociation constant and kinetic quantities such as association rate constant for the triplex formation. These results showed that the chemical modification, particularly at backbone, affected the thermodynamic and kinetic quantities of triplex formation. We attempted to investigate the molecular mechanism of that effect by computational analysis. We performed quantum-chemical calculations for the modified DNA to obtain partial atomic charges and conformation of DNA. We found that the phosphorothioation of DNA has significant effect on the charges and conformation. We also performed computer simulation of DNA to calculate its average conformation and fluctuation, by using a new algorithm for conformational sampling. The chemical modification affected the average conformation and fluctuation of DNA depending on the location of the modification. These results suggest that the chemical modification may affect the stability and specificity of triplex DNA formation through the changes in structure and property of DNA. In order to understand the biological role of triplex DNA in cell, we made biochemical and functional analyses of MAZ protein, which binds to triplex DNA. This protein acts as a transcription factor and regulates the expression of c-myc gene. We also examined the effect of chemical modification of DNA on the binding and transcriptional activities of an oncogene product, Myb. We found that the modification destabilized the DNA and abolished the Myb binding. The present experimental and computational studies of triplex DNA have laid a basis for the design of antisense DNA, which inhibits expression of genes.

  • Research Products

    (10 results)

All Other

All Publications (10 results)

  • [Publications] T.Kittaka, et al.: "Oligonucleotides containing a 6-substituted pyrimidine base : a design for Myb inhibitors"Nucleosides Nucleotides. 18. 2769-2783 (1999)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] T.Kittaka, et al.: "Introduction of 6-formylcytidine into a Myb binding sequence"Nucleosides Nucleotides. 18. 2769-2783 (1999)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Uchida S. et al.: "Transcriptional regulation of the CLC-K1 promoter by myc-associated zinc finger protein and kidney-enriched Kruppel-like factor, a novel zinc finger repressor"Mol. Cell Biol.. 19. 7319-7331 (2000)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Song J.et al.: "The multiple roles of the transcription factors MAZ and Pur-1, two proteins encoded by housekeeping genes"Current Genomics. 1. 175-187 (2001)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Song J.et al.: "Two consecutive zinc fingers in Sp1 and in MAZ are essential for interactions with cis-elements"J. Biol. Chem.. (印刷中). (2001)

    • Description
      「研究成果報告書概要(和文)」より
  • [Publications] Kittaka, T. Kuze, H. Tanaka, X Miyasaka, K. Hirose, T. Yoshida, A. ; Sarai, T. Yasukawa, S. Ishii: "Oligonucleotides containing a 6-substituted pyrimidine base : a design for Mybinhibitors."Nucleosides Nucleotides. 18. 1501-1502 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Kittaka, T. Kuze, M. Amano, H. Tanaka, T. Miyasaka, K. Hirose, JT. Yoshida, A. Sarai, T. Yasukawa, S. Ishii: "Introduction of 6-formylcytidine into a Myb binding sequence."Nucleosides Nucleotides. 18. 2769-2783 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Uchida, S., Tanaka, Y, Ito, H., Saito-Ohara, R, Yokoyama, K., Sasaki, S., and Maruno, F: "Transciptional regulation of the CLC-KI promoter by MAZ and KKLF, a novel kruppel -like zinc finger repressor"Mol. Cell. Biol.. 20. 7319-7331 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Song, J., Tsutsui, H., Jin, C., Ugai, H., and Yokoyama, K,: "The multiple roles of the transcriptional factors MAZ and Pur-1, two protein encoded by housekeeping genes."Current Genomics. 1. 175-187 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Publications] Song J, Ugai H, Qgawa K, Wang' Sarai A, Obata Y, Kanazawa I Sun K, Itakura K, and Yokoyama KK: "Two consecutive zinc fingers in Sp1 and in MAZ are essential for interactions with cis-elements."J. Biol. Chem.. (in press). (2001)

    • Description
      「研究成果報告書概要(欧文)」より

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Published: 2003-09-17  

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